I’m just gonna copy-paste some stuff from the Disqus comments on that post to start this off:

GLaDONT: I believe pokeballs are the bad thing that happened in the past, at some point along the way we developed storage devices that maybe at the time had unintended side affects of affecting a pokemon’s nature. We have seen mutilpe times in the anime unwilling pokemn turning 180 after capture. I think the idea is pokeballs can make any pokemon your partner whether it wants it or not, making what may have once been a voluntary friendship into something darker.

Pokémaniac Chris: I don’t really want to devote all that much attention to poking holes in the ‘brainwashing’ thing, *or* to plugging those holes; mostly my problem with it is that it seems *too obvious*. Whatever’s going on, I think, has to have been more subtle in order to go unnoticed. At the moment, I think that Pokéballs are a problem because they symbolise the way industrialisation and modernity have changed Pokémon training. Without Pokéballs, it’s hard for one person to keep a large number of Pokémon, it’s hard for people to travel with Pokémon, it’s hard to create spaces in towns and cities where you can exclude Pokémon, and it’s hard to ignore your Pokémon even for a short time. None of these things are direct and necessary consequences of using Pokéballs, but they’re ways in which the relationship *can* change and develop because of them.

I don’t believe that Pokéballs ‘brainwash’ Pokémon in any absolute sense.  I do wonder whether it’s possible they could alter Pokémon’s brain chemistry in a way that makes them more suggestible – not so they actually can’t disobey an order or anything like that, more so that, in most circumstances, most Pokémon will be easily persuaded to obey orders.  I don’t think that’s what happens, but I also don’t think it’s easy to prove it’s not happening, and I really don’t want to start rewatching anime episodes hunting for examples and counterexamples, because seriously f&$% that.  Mostly I think that my sort of explanation is just more consistent with the themes of the series – the way it presents the contrasts between tradition and progress, and between nature and civilisation.  Some kind of scenario where Pokéballs alter the brain chemistry of Pokémon almost seems to necessitate a sort of bizarre conspiracy on the part of the makers of Pokéballs – because it seems clear that most people aren’t aware of any compulsion or mind-altering influence – or an even more bizarre accident of the workings of the technology that was somehow never noticed.  That’s why I prefer to imagine that the problems with Pokéballs stem from things you might not even think of when you first started using them, or even from things that seem obviously beneficial at first, but turn out to be double-edged swords.  Pokéballs reduce the constraints of food and space – which means that you can have more Pokémon, and will inevitably pay less attention to each one (early excesses in this regard may have led to criminal neglect that ultimately resulted in laws limiting an active party to six Pokémon – in fact I think this is a much more likely explanation than anything related to battles, since the vast majority of battles use far fewer Pokémon than six anyway).  Pokéballs allow you to travel easily with Pokémon – which means you can take them far away from their native habitats and don’t have to think too hard about what you’re doing.  Once Pokéballs are in common use, it’s easy for civic governments to enforce legislation (if they choose to enact it) that excludes Pokémon from certain buildings or areas, because asking someone just to recall their Pokémon is never going to seem like an unreasonable request.  Pokémon can and sometimes do leave their balls without being called, but they also can’t seem to ignore being recalled unless they can actually dodge the beam, so if you just don’t want to deal with them right now you can always enforce a short ‘time out.’  None of this actually compels Pokémon to do anything; all of it puts trainers in a greater position of implicit authority than they would otherwise have – and to me that’s actually a much more interesting situation than a global brainwashing conspiracy.

I’m actually not totally clear on what you’re asking me here, but I can talk about the Cave of Dragonflies article.  I’ve been pointed at it before; it’s interesting.  More than a little ‘out there,’ but it’s not like some of my ideas aren’t just as weird, and more to the point it never claims to be authoritative – just an interesting and speculative way of interpreting what we see.  There are things in it that I like and things that I’m more sceptical about.  Broadly speaking, the narrative makes a lot of sense – humans befriend weak Pokémon; through cooperation and the strategic skills of humans, weak Pokémon become strong; humans formalise and codify strategies to increase their advantages; settlements become secure; travel and communication become freer and easier; after Pokéballs are invented, everything becomes streamlined.  In particular, the notion that wild Pokémon fight trainers because they’re looking for partners, and submit to capture if and when they feel a trainer is worthy, has a lot in common with my own ideas.

One thing that bothers me is the idea that Pokémon have a genetic imperative to seek out competition and that this is universal across all species, because it seems pretty clear that their temperaments and their attitudes to battle vary a lot more than that – it’s hard to imagine characterising, say, Slowpoke or Oddish as “fiercely competitive and [desiring] strength for its own sake.”  I think it’s easier just to say that not all Pokémon do like fighting, which fits well enough with what we see in the anime – and this article actually does say something similar later on, noting that Pokémon who don’t like fighting and don’t want trainers will normally just stay out of our way.  Another potentially objectionable point is that the way apricorns are imagined to work is just so… bizarre.  It’s certainly clever, but the way apricorns are treated in the games and anime seems totally incongruous with the idea that they can eat Pokémon (my own suggestion for dealing with the first apricorn Pokéballs is that their bizarre properties are brought out by the Natural Gift attack, since we know that Natural Gift can make berries do all kinds of weird things).  But yeah.  It’s interesting.  Worth the read.

Y’know, I was rereading some old questions and comments the other day and someone else actually made a similar suggestion ages ago; I meant to give it more thought than I did, but I sort of forgot about it and never picked it up again, which is a shame because it’s a really interesting idea.  Let’s remedy that, shall we?

In ecology, there’s a concept called ‘succession,’ which describes the way ecosystems respond to change.  After an ecosystem is disrupted or damaged – by a forest fire, an earthquake, human activity, whatever – the first organisms to recolonise the damaged area are ‘pioneer species,’ very basic, hardy organisms that can survive anywhere because they just don’t do much, things like lichens, mosses, and soil bacteria.  They’re followed by species that depend on them – ants, earthworms, shrubs and grasses, then small vertebrate animals after that.  All those boring little organisms are necessary to build up the rich soil that allows larger plants to grow, and those plants are necessary to support large herbivores, and a wide variety of herbivores is necessary to support things like big apex predators, so the community builds up slowly and gets more and more complex.  In ecological theory, the ultimate result of succession is a ‘climax community’ – a complicated, high-biodiversity ecosystem containing numerous specialised organisms which is in a state of equilibrium and, assuming it’s left alone, won’t develop any further, because that particular combination of species is perfectly balanced for the local climate.  There’s actually some debate about whether true climax communities really exist; some ecologists think that all ecosystems are in a state of constant change, or that the kind of stability envisioned by climax theory would take centuries or even millennia to develop, which is simply unrealistic (even without human intervention, natural disasters disturb communities all the time).

Basically, then – high level and particularly evolved Pokémon are only likely to be found in more ‘mature’ ecosystems, because that kind of longevity and prosperity depends on having a rich environment filled with things like nutritious high-energy plants and specialised organisms with complex interactions.  Moreover, because it takes a long time for Pokémon to level in the wild, those conditions have to be sustained for years, even decades, before you actually start seeing really powerful ones.  Once they do exist, though, their very presence stabilises the ecosystem because their powers allow them to make efficient use of resources and provide buffering against natural disasters – or, in some other cases (I’m looking at you, Tyranitar), they might throw the whole thing out of whack again and begin the process of succession anew!